Thesis (Ph. D.)--University of Wisconsin, 1967. / Typescript. Vita. "A perturbation theory of isoelectronic molecules," by Tai Yup Chang and W. Byers Brown. Reprinted from Theoret. Chim. Acta (Berl.) v. 4, 393-407 (1966): leaves 131-145. eContent provider-neutral record in process. Description based on print version record. Includes bibliography.

Thesis (Ph. D.)--University of Michigan, 1945. / "Reprinted from the Journal of chemical physics, vol. 14, no. 10 ... October, 1946." Master microform held by: UnM. Bibliographical foot-notes.

Thesis (Ph. D.)--University of Delaware, 2007. / Principal faculty advisor: Dionisios G. Vlachos, Dept. of Chemical Engineering. Includes bibliographical references.

Thesis (Ph. D.)--University of Chicago, 1916. / "Private Edition, Distributed by the University of Chicago Libraries, Chicago, Illinois." "Reprinted from the Physical Review, N.S., Vol. X, No. 4, October 1917." Includes bibliographical references. Also available on the Internet.

AA9 proteins are metallo-enzymes which are crucial for the early stages of cellulose degradation. AA9 proteins have been suggested to cleave glycosidic bonds linking cellulose through the use of their Cu2+ coordinating active site. AA9 proteins possess different regioselectivities depending on the resulting cleavage they form and as result, are grouped accordingly. Type 1 AA9 proteins cleave the C1 carbon of cellulose while Type 2 AA9 proteins cleave the C4 carbon and Type 3 AA9 proteins cleave either C1 or C4 carbons. The steric congestion of the AA9 active site has been proposed to be a contributor to the observed regioselectivity. As such, a bioinformatics characterisation of type-specific sequence and structural features was performed. Initially AA9 protein sequences were obtained from the Pfam database and multiple sequence alignment was performed. The sequences were phylogenetically characterised and sequences were grouped into their respective types and sub-groups were identified. A selection analysis was performed on AA9 LPMO types to determine the selective pressure acting on AA9 protein residues. Motif discovery was then performed to identify conserved sequence motifs in AA9 proteins. Once type-specific sequence features were identified structural mapping was performed to assess possible effects on substrate interaction. Physicochemical property analysis was also performed to assess biochemical differences between AA9 LPMO types. Molecular dynamics (MD) simulations were then employed to dynamically assess the consequences of the discovered type-specific features on AA9-cellulose interaction. Due to the absence of AA9 specific force field parameters MD simulations were not readily applicable. As a result, Potential Energy Surface (PES) scans were performed to evaluate the force field parameters for the AA9 active site using the PM6 semi empirical approach and least squares fitting. A Type 1 AA9 active site was constructed from the crystal structure 4B5Q, encompassing only the Cu2+ coordinating residues, the Cu2+ ion and two water residues. Due to the similarity in AA9 active sites, the Type force field parameters were validated on all three AA9 LPMO types. Two MD simulations for each AA9 LPMO types were conducted using two separate Lennard-Jones parameter sets. Once completed, the MD trajectories were analysed for various features including the RMSD, RMSF, radius of gyration, coordination during simulation, hydrogen bonding, secondary structure conservation and overall protein movement. Force field parameters were successfully evaluated and validated for AA9 proteins. MD simulations of AA9 proteins were able to reveal the presence of unique type-specific binding modes of AA9 active sites to cellulose. These binding modes were characterised by the presence of unique type-specific loops which were present in Type 2 and 3 AA9 proteins but not in Type 1 AA9 proteins. The loops were found to result in steric congestion that affects how the Cu2+ ion interacts with cellulose. As a result, Cu2+ binding to cellulose was observed for Type 1 and not Type 2 and 3 AA9 proteins. In this study force field parameters have been evaluated for the Type 1 active site of AA9 proteins and this parameters were evaluated on all three types and binding. Future work will focus on identifying the nature of the reactive oxygen species and performing QM/MM calculations to elucidate the reactive mechanism of all three AA9 LPMO types.

This master thesis is focused on theoretical study of the Cy3 and Cy5 dyes and their interactions with DNA. The main aim was to find the mot populated conformations of the Cy3-DNA and Cy5-DNA complexes. A comparison with the experimental structure was also done and the influence of the cyanine dyes on the conformational changes of the DNA chain was evaluated.

Nuclear magnetic resonance absorption and spin-lattice relaxation time measurements have been carried out on the tropolone salt of t-butylamine, (CH₃)₃CN⁺H₃Tr⁻ (Tr ⁻= tropolonate ion, C₇H₅0₂⁻), the choline salts, (CH₃)₃NCH₂CH₂OH. X⁻ (x⁻ = Cl⁻, Br , I , ClO₄ ⁻) and the trimethylamine-phosphorous penta-fluoride adduct, (CH₃)₃NPF₅, in order to study molecular motion and phase transitions in these systems in the solid state. Activation energies and rate parameters associated with the motional processes are reported. Proton magnetic resonance (pmr) absorption second moments and proton spin-lattice relaxation times in the Zeeman frame (T₁) in the temperature range 66K - 425K for the solid (CH₃)₃CNH₃Tr⁻ show that the molecule is rigid on the nmr timescale at the lowest temperature studied, while at higher temperatures rotation of methyls about their C₃ symmetry axes is found to set in first, followed by an additional composite motion involving reorientation of both the t-butyl group and the NH₃ group about the C-N bond. A proton study in the partially deuterated (-ND₃) analogue has enabled the relaxation effects of the latter two motions to be separated, and, by fitting the T₁, data for the two compounds to appropriate relaxation rate expressions, activational energy barriers for the abovementioned motional processes have been determined. It has also been suggested that the t-butyl group and the NH₃ group rotate independently about the C-N bond rather than as one unit. Proton spin-lattice relaxation time measurements in both the Zeeman and rotating frames of reference (T₁ and T₁[sub p]) for the four choline salts and second moments of the pmr absorption for the perchlorate have enabled the following motional processes to be identified: (i) rotation of the methyl groups at low temperatures followed successively by, (ii) the onset of motion of the NMe₃ moiety about the long chain C-N axis (denoted C₃), (iii) general reorientation of the whole choline cation, (iv) additional slow motion of the long chain (CH₂CH₂OH in the case of the chloride and bromide, and (v) diffusion of the choline ion in the case of the iodide and perchlorate. From a quantitative analysis of the and data, activation energies for the above types of motion are determined. A crystal-crystal phase transition known to occur at 353, 364 and 362K in the chloride, bromide and iodide, respectively, has been confirmed. A similar transition has been discovered in the perchlorate, and is found to occur at a much lower temperature (272K). Evidence has also been presented for a further crystal-crystal phase transition in choline iodide at 430K, at which point a "quenching" of the diffusional process is found in this structure. In the adduct (CH₃)₃NPF₅, studies of proton and fluorine nmr absorption spectra and measurements have shown that (i) at 4.2K the molecule is 'rigid1, (ii) C₃ reorientation of one of the methyls and reorientation of the PF₅ group about the P-N bond cause a ¹H and ¹⁹F nmr line narrowing, (iii) this is followed by the C₃ rotation of the other two methyl groups together with the rotation of the (CH₃)₃N group about the P-N bond. These are confirmed by a successful simulation of the observed pmr lineshapes at 4.2K and at 77K. The proton and fluorine T₁ data show the ¹H and ¹⁹F spins to be strongly coupled. A study of fluorine T₁ in the fully deuterated compound, (CD₃)₃NPF₅ has enabled the analysis of the overall T₁ data to be simplified. The observed trends in the T₁ data are seen to be well explained by the theory for a coupled spin system of two unlike spins. / Science, Faculty of / Chemistry, Department of / Graduate

Molecular dynamics (MD) simulations play a pivotal role in understanding the behavior of complex molecular systems, offering insights into the behavior of molecules at the atomic level, while their accuracy heavily depends on the force field parameters used. In this study, we present an investigation focusing on two distinct aspects: the validation of MD simulations for plasticizers, and the development of a quantitative structure property relationship (QSPR) model to fit data derived from these simulations. Our goal is to provide researchers with valuable insights into the choice of force fields to improve the accuracy of simulations in various scientific domains and the modeling of prediction of properties of plasticizers. In the first part, We explore various aspects of validation, including force field accuracy, equilibration protocols, and comparison of simulation results of plasticizers with experimental data. We begin by validating popular force fields: PCFF, SciPCFF and COMPASS. By examining the behavior of small molecules, we aim to ensure the reliability of force fields for these compounds with specific desired functional groups. Density, heat of vaporization and shear viscosity results are used for the validation of force fields. We compare various equilibration methods and their impact on simulation outcomes to address issues related to system stability and convergence, for enhancing the efficiency and accuracy of simulations. The second part of our research shifts focus to the prediction modeling of plasticizers, a class of chemical additives commonly used in the polymer industry to enhance the flexibility of plastic materials. We attempt to predict the solubility parameters of plasticizers by QSPR. Simple counts, Wiener Indices and Randic Branching Indices are used as descriptors in the QSPR. Our prediction model results show the dependence of plasticizers on the descriptors while the QSPR equation obtained from our current data-set with five descriptors has the R2 = 0.73. In conclusion, this comprehensive study bridges the gap between force field validation and equilibration for plasticizers. Moreover, the integration of QSPR models offers insights to a robust approach for predicting molecular behaviors. / Thesis / Master of Applied Science (MASc)

Interest in nanoscale heat and mass transport has been augmented through current trends in nanotechnology research. The theme of this dissertation is to characterize electric charge, mass and thermal transport at the nanoscale using a fundamental molecular simulation method, namely molecular dynamics. This dissertation reports simulations of (1) ion intake by carbon nanotubes, (2) hydrogen storage in carbon nanotubes, (3) carbon nanotube growth and (4) nanoscale heat transfer. Ion transport is investigated in the context of desalination of a polar solution using charged carbon nanotubes. Simulations demonstrate that when either a spatially or temporally alternating charge distribution is applied, ion intake into the nanotubes is minimal. Thus, the charge distribution can either be maintained constant (for ion encapsulation) or varied (for water intake) in order to achieve different effects. Next, as an application of mass transport, the hydrogen storage characteristics of carbon nanotubes under modified conditions is reported. The findings presented in this dissertation suggest a significant increment in storage in the presence of alkali metals. The dependence of storage on the external thermodynamic conditions is analyzed and the optimal range of operating conditions is identified. Another application of mass transport is the growth mode of carbon nanostructures (viz. tip growth and base growth). A correct prediction of the dominant growth mode depends on the energy gain due to the addition of C-atoms from the carbon-metal catalyst solution to the graphene sheets forming the carbon nanostructures. This energy gain is evaluated through molecular dynamics simulations. The results suggest tip growth for Ni and base growth for Fe catalysts. Finally, unsteady nanoscale thermal transport at solid-fluid interfaces is simulated using non-equilibrium molecular dynamics simulations. It is found that the simulated temperature evolution deviates from an analytical continuum solution due to the overall system heterogeneity. Temperature discontinuities are observed between the solid-like interfaces and their neighboring fluid molecules. With an increase in the temperature of the solid wall the interfacial thermal resistance decreases. / Ph. D.

The prediction of an atomistic system's macroscopic observables from microscopic physical characteristics is often intractable, either by theory or computation, due to the intrinsic complexity of the underlying dynamical rules. This complexity can be simplified by identifying key mechanisms that drive behavior and considering the system in a reduced representation that captures these mechanisms. Through theory, this thesis examines complex relationships in structured assembly and reaction mechanisms that occur when effective interactions are applied to mesoscale structures. In the first part of this thesis, the structure and assembly of soft matter systems are characterized while varying the interpenetrability of the constituent particles. The nature of the underlying softness allows these systems to be packed at ever higher density, albeit with an increasing penalty in energy. Stochastic equations of motion are developed in which mesoscopic structures are mapped to single degrees of freedom through a coarse-graining procedure. The effective interactions between these coarse-grained sites are modeled using stochastic potentials that capture the spatial behavior observed in systems governed by deterministic bounded potentials. The second part of this thesis presents advancements in time-dependent transition state theory, focusing on chemical reactions that are induced by oscillatory external forces. The optimal dividing surface for a model driven reaction is constructed over a transition state trajectory. The stability of the transition state trajectory is found to directly dictate the reaction rate, and it is thus the fundamental and singular object needed to predict barrier-crossing rates in periodically driven chemical reactions. This thesis demonstrates that using minimalist models to examine these complex systems can provide valuable insight into the dynamical mechanisms that drive behavior.